Abstract The aim of the Parasite Genetics Core (PGC) will be to enable the Southern and Central Africa ICEMR to apply state-of-the-art next generation sequencing and bioinformatic tools to better understand malaria epidemiology and the impact of control interventions in Zambia, Zimbabwe and the Democratic Republic of the Congo (DRC). Specifically, the long term objectives and goals of the PGC are to provide; laboratory analyses of parasites from ICEMR samples, bioinformatic processing of next-generation sequencing data for projects in this previous aim, training for investigators in this and other ICEMRs, quality control of genetic data and samples for analyses conducted at field sites. The PGC will provide a centralized laboratory for genetic analysis of parasite samples from all three projects within the ICEMR. These laboratory analyses will focus primarily on next generation sequencing techniques: (1) amplicon deep sequencing, (2) pooled amplicon deep sequencing and (3) PoolSeq. The proposed laboratory work for the PGC includes activities in: Project A: Malaria Control in Southern and Central Africa (Epidemiology), Project B: Intractable Malaria Vector Populations and Residual Transmission in Southern and Central Africa (Transmission I), and Project C: Achieving, Sustaining, and Documenting Malaria Elimination (Transmission II). Data analysis of next generation sequencing is computationally intensive and rapidly developing. Thus, a portion of the core will be dedicated to assisting investigators with these state-of-the art analyses. The facilities at the PGC will allow us to host investigators from the Southern and Central Africa ICEMR, as well as collaborate with investigators from other ICEMRs, in order for the techniques to be transferred to other institutions. This will allow us to potentially foster cross ICEMR collaboration and to train non-US based scientists on state of the art population genetics laboratory and analysis methods.